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Coucke Q, Parveen N, Fernández GS, Qian C, Hofkens J, Debyser Z, Hendrix J. Particle-based phasor-FLIM-FRET resolves protein-protein interactions inside single viral particles. BIOPHYSICAL REPORTS 2023; 3:100122. [PMID: 37649577 PMCID: PMC10463199 DOI: 10.1016/j.bpr.2023.100122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/07/2023] [Indexed: 09/01/2023]
Abstract
Fluorescence lifetime imaging microscopy (FLIM) is a popular modality to create additional contrast in fluorescence images. By carefully analyzing pixel-based nanosecond lifetime patterns, FLIM allows studying complex molecular populations. At the single-molecule or single-particle level, however, image series often suffer from low signal intensities per pixel, rendering it difficult to quantitatively disentangle different lifetime species, such as during Förster resonance energy transfer (FRET) analysis in the presence of a significant donor-only fraction. In this article we investigate whether an object localization strategy and the phasor approach to FLIM have beneficial effects when carrying out FRET analyses of single particles. Using simulations, we first showed that an average of ∼300 photons, spread over the different pixels encompassing single fluorescing particles and without background, is enough to determine a correct phasor signature (SD < 5% for a 4-ns lifetime). For immobilized single- or double-labeled dsDNA molecules, we next validated that particle-based phasor-FLIM-FRET readily allows estimating fluorescence lifetimes and FRET from single molecules. Thirdly, we applied particle-based phasor-FLIM-FRET to investigate protein-protein interactions in subdiffraction HIV-1 viral particles. To do this, we first quantitatively compared the fluorescence brightness, lifetime, and photostability of different popular fluorescent protein-based FRET probes when genetically fused to the HIV-1 integrase enzyme in viral particles, and conclude that eGFP, mTurquoise2, and mScarlet perform best. Finally, for viral particles coexpressing FRET-donor/acceptor-labeled IN, we determined the absolute FRET efficiency of IN oligomers. Available in a convenient open-source graphical user interface, we believe that particle-based phasor-FLIM-FRET is a promising tool to provide detailed insights in samples suffering from low overall signal intensities.
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Affiliation(s)
- Quinten Coucke
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Nagma Parveen
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Guillermo Solís Fernández
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
- UFIEC, National Institute of Health Carlos III, Madrid, Spain
| | - Chen Qian
- Department of Chemistry, Center for Nano Science (CENS), Center for Integrated Protein Science Munich (CIPSM), and Nanosystems Initiative Munich (NIM), Ludwig Maximilians-Universität München, Munich, Germany
| | - Johan Hofkens
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Zeger Debyser
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Jelle Hendrix
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute, Hasselt University, Hasselt, Belgium
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Franssen WMJ, Treibel TA, Seraphim A, Weingärtner S, Terenzi C. Model-free phasor image analysis of quantitative myocardial T 1 mapping. Sci Rep 2022; 12:19840. [PMID: 36400794 PMCID: PMC9674690 DOI: 10.1038/s41598-022-23872-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 11/07/2022] [Indexed: 11/19/2022] Open
Abstract
Model-free phasor image analysis, well established in fluorescence lifetime imaging and only recently applied to qMRI [Formula: see text] data processing, is here adapted and validated for myocardial qMRI [Formula: see text] mapping. Contrarily to routine mono-exponential fitting procedures, phasor enables mapping the lifetime information from all image voxels to a single plot, without resorting to any regression fitting analysis, and describing multi-exponential qMRI decays without biases due to violated modelling assumptions. In this feasibility study, we test the performance of our recently developed full-harmonics phasor method for unravelling partial-volume effects, motion or pathological tissue alteration, respectively on a numerically-simulated dataset, a healthy subject scan, and two pilot patient datasets. Our results show that phasor analysis can be used, as alternative method to fitting analysis or other model-free approaches, to identify motion artifacts or partial-volume effects at the myocardium-blood interface as characteristic deviations, or delineations of scar and remote myocardial tissue in patient data.
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Affiliation(s)
- Wouter M. J. Franssen
- grid.4818.50000 0001 0791 5666Laboratory of Biophysics, Wageningen University and Research, Wageningen, The Netherlands
| | - Thomas A. Treibel
- grid.83440.3b0000000121901201Institute of Cardiovascular Science, University College London, London, UK ,grid.416353.60000 0000 9244 0345Department of Cardiology, St Bartholomew’s Hospital, Barts Health NHS Trust, London, UK
| | - Andreas Seraphim
- grid.83440.3b0000000121901201Institute of Cardiovascular Science, University College London, London, UK ,grid.416353.60000 0000 9244 0345Department of Cardiology, St Bartholomew’s Hospital, Barts Health NHS Trust, London, UK
| | - Sebastian Weingärtner
- grid.5292.c0000 0001 2097 4740Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Camilla Terenzi
- grid.4818.50000 0001 0791 5666Laboratory of Biophysics, Wageningen University and Research, Wageningen, The Netherlands
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Mishra YG, Manavathi B. Focal adhesion dynamics in cellular function and disease. Cell Signal 2021; 85:110046. [PMID: 34004332 DOI: 10.1016/j.cellsig.2021.110046] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023]
Abstract
Acting as a bridge between the cytoskeleton of the cell and the extra cellular matrix (ECM), the cell-ECM adhesions with integrins at their core, play a major role in cell signalling to direct mechanotransduction, cell migration, cell cycle progression, proliferation, differentiation, growth and repair. Biochemically, these adhesions are composed of diverse, yet an organised group of structural proteins, receptors, adaptors, various enzymes including protein kinases, phosphatases, GTPases, proteases, etc. as well as scaffolding molecules. The major integrin adhesion complexes (IACs) characterised are focal adhesions (FAs), invadosomes (podosomes and invadopodia), hemidesmosomes (HDs) and reticular adhesions (RAs). The varied composition and regulation of the IACs and their signalling, apart from being an integral part of normal cell survival, has been shown to be of paramount importance in various developmental and pathological processes. This review per-illustrates the recent advancements in the research of IACs, their crucial roles in normal as well as diseased states. We have also touched on few of the various methods that have been developed over the years to visualise IACs, measure the forces they exert and study their signalling and molecular composition. Having such pertinent roles in the context of various pathologies, these IACs need to be understood and studied to develop therapeutical targets. We have given an update to the studies done in recent years and described various techniques which have been applied to study these structures, thereby, providing context in furthering research with respect to IAC targeted therapeutics.
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Affiliation(s)
- Yasaswi Gayatri Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Bramanandam Manavathi
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
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Bauer TJ, Gombocz E, Krüger M, Sahana J, Corydon TJ, Bauer J, Infanger M, Grimm D. Augmenting cancer cell proteomics with cellular images - A semantic approach to understand focal adhesion. J Biomed Inform 2019; 100:103320. [PMID: 31669288 DOI: 10.1016/j.jbi.2019.103320] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 09/23/2019] [Accepted: 10/23/2019] [Indexed: 01/13/2023]
Abstract
If monolayers of cancer cells are exposed to microgravity, some of the cells cease adhering to the bottom of a culture flask and join three-dimensional aggregates floating in the culture medium. Searching reasons for this change in phenotype, we performed proteome analyses and learnt that accumulation and posttranslational modification of proteins involved in cell-matrix and cell-cell adhesion are affected. To further investigate these proteins, we developed a methodology to find histological images about focal adhesion complex (FA) proteins. Selecting proteins expressed by human FTC-133 and MCF-7 cancer cells and known to be incorporated in FA, we transformed the experimental data to RDF to establish a core semantic knowledgebase. Applying iterative SPARQL queries to Linked Open Databases, we augmented these data with additional functional, transformation- and aggregation-related relationships. Using reasoning, we retrieved publications with images about the spatial arrangement of proteins incorporated in FA. Contextualizing those images enabled us to gain insights about FA of cells changing their site of growth, and to independently validate our experimental results. This new way to link experimental proteome data to biomedical knowledge from various sources via searching images may generally be applied in science when images are a tool of knowledge dissemination.
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Affiliation(s)
- Thomas J Bauer
- Clinic for Plastic, Aesthetic and Hand Surgery, Otto-von-Guericke-University Magdeburg, D-39120 Magdeburg, Germany.
| | - Erich Gombocz
- Melissa Informatics, 2550 Ninth Street, Suite 114, Berkeley, CA, USA.
| | - Marcus Krüger
- Clinic for Plastic, Aesthetic and Hand Surgery, Otto-von-Guericke-University Magdeburg, D-39120 Magdeburg, Germany.
| | - Jayashree Sahana
- Department of Biomedicine, Aarhus University, Hoeg-Guldbergsgade 10, DK-8000 Aarhus C, Denmark.
| | - Thomas J Corydon
- Department of Biomedicine, Aarhus University, Hoeg-Guldbergsgade 10, DK-8000 Aarhus C, Denmark; Department of Ophthalmology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, DK-8200 Aarhus N, Denmark.
| | - Johann Bauer
- Max-Planck Institute of Biochemistry, D-82152 Martinsried, Germany.
| | - Manfred Infanger
- Clinic for Plastic, Aesthetic and Hand Surgery, Otto-von-Guericke-University Magdeburg, D-39120 Magdeburg, Germany.
| | - Daniela Grimm
- Clinic for Plastic, Aesthetic and Hand Surgery, Otto-von-Guericke-University Magdeburg, D-39120 Magdeburg, Germany; Department of Biomedicine, Aarhus University, Hoeg-Guldbergsgade 10, DK-8000 Aarhus C, Denmark; Gravitational Biology and Translational Regenerative Medicine, Faculty of Medicine and Mechanical Engineering, Otto-von-Guericke-University-Magdeburg, D-39120 Magdeburg, Germany.
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Wang Q, Delcorde J, Tang T, Downey GP, McCulloch CA. Regulation of IL-1 signaling through control of focal adhesion assembly. FASEB J 2018; 32:3119-3132. [PMID: 29401618 DOI: 10.1096/fj.201700966r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
IL-1 signaling is adhesion-restricted in many cell types, but the mechanism that drives it is not defined. We screened for proteins recruited to nascent adhesions in IL-1-treated human fibroblasts with tandem mass tag-mass spectrometry. We used fibronectin bead preparations to enrich 10 actin-associated proteins. There was a 1.2 times log 2-fold enrichment of actin capping protein (ACP) at 30 min after IL-1 stimulation. Knockdown (KD) of ACP by siRNA reduced IL-1-induced ERK activation(by 56%, matrix metalloproteinase-3 (MMP-3) expression by 48%, and MMP-9 expression by 62% (in all reductions, P < 0.01). Confocal or structured illumination microscopy showed that ACP was diffused throughout the cytosol but strongly accumulated at the ruffled border of spreading cells. ACP colocalized with nascent paxillin- and vinculin-containing adhesions at the ruffled border, but not with mature adhesions in the center. ACP KD promoted the formation of large, stable adhesions. Immunoprecipitation and proximity ligation analysis showed that ACP was associated with the IL-1 signal transduction proteins myeloid differentiation factor 88 (MyD88) and IL-1 receptor-associated kinase (IRAK) at the ruffled border of the leading edge. IL-1-induced phospho-ERK and MyD88 or IRAK colocalized at the leading edge. We concluded that ACP is required for recruitment and function of IL-1 signaling complexes in nascent adhesions at the leading edge of the cell.-Wang, Q., Delcorde, J., Tang, T., Downey, G. P., McCulloch, C. A. Regulation of IL-1 signaling through control of focal adhesion assembly.
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Affiliation(s)
- Qin Wang
- Matrix Dynamics Group, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Julie Delcorde
- Matrix Dynamics Group, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Tracy Tang
- Matrix Dynamics Group, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Gregory P Downey
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, National Jewish Health, Denver, Colorado, USA
| | - Christopher A McCulloch
- Matrix Dynamics Group, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
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Chang SJ, Chen YC, Yang CH, Huang SC, Huang HK, Li CC, Harn HIC, Chiu WT. Revealing the three dimensional architecture of focal adhesion components to explain Ca 2+-mediated turnover of focal adhesions. Biochim Biophys Acta Gen Subj 2017; 1861:624-635. [PMID: 28063985 DOI: 10.1016/j.bbagen.2017.01.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 12/07/2016] [Accepted: 01/03/2017] [Indexed: 10/20/2022]
Abstract
BACKGROUND Focal adhesions (FAs) are large, dynamic protein complexes located close to the plasma membrane, which serve as the mechanical linkages and a biochemical signaling hub of cells. The coordinated and dynamic regulation of focal adhesion is required for cell migration. Degradation, or turnover, of FAs is a major event at the trailing edge of a migratory cell, and is mediated by Ca2+/calpain-dependent proteolysis and disassembly. Here, we investigated how Ca2+ influx induces cascades of FA turnover in living cells. METHODS Images obtained with a total internal reflection fluorescence microscope (TIRFM) showed that Ca2+ ions induce different processes in the FA molecules focal adhesion kinase (FAK), paxillin, vinculin, and talin. Three mutated calpain-resistant FA molecules, FAK-V744G, paxillin-S95G, and talin-L432G, were used to clarify the role of each FA molecule in FA turnover. RESULTS Vinculin was resistant to degradation and was not significantly affected by the presence of mutated calpain-resistant FA molecules. In contrast, talin was more sensitive to calpain-mediated turnover than the other molecules. Three-dimensional (3D) fluorescence imaging and immunoblotting demonstrated that outer FA molecules were more sensitive to calpain-mediated proteolysis than internal FA molecules. Furthermore, cell contraction is not involved in degradation of FA. CONCLUSIONS These results suggest that Ca2+-mediated degradation of FAs was mediated by both proteolysis and disassembly. The 3D architecture of FAs is related to the different dynamics of FA molecule degradation during Ca2+-mediated FA turnover. GENERAL SIGNIFICANCE This study will help us to clearly understand the underlying mechanism of focal adhesion turnover by Ca2+.
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Affiliation(s)
- Shu-Jing Chang
- Department of Biomedical Engineering, National Cheng Kung University, Tainan 701, Taiwan
| | - Ying-Chi Chen
- Department of Biomedical Engineering, National Cheng Kung University, Tainan 701, Taiwan
| | - Chi-Hsun Yang
- Department of Biomedical Engineering, National Cheng Kung University, Tainan 701, Taiwan
| | - Soon-Cen Huang
- Department of Obstetrics and Gynecology, Chi Mei Medical Center, Liouying Campus, Tainan 736, Taiwan
| | - Ho-Kai Huang
- Department of Biomedical Engineering, National Cheng Kung University, Tainan 701, Taiwan
| | - Chun-Chun Li
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Hans I-Chen Harn
- Institute of Basic Medical Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Wen-Tai Chiu
- Department of Biomedical Engineering, National Cheng Kung University, Tainan 701, Taiwan; Institute of Basic Medical Sciences, National Cheng Kung University, Tainan 701, Taiwan; Medical Device Innovation Center, National Cheng Kung University, Tainan 701, Taiwan.
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Nordenfelt P, Elliott HL, Springer TA. Coordinated integrin activation by actin-dependent force during T-cell migration. Nat Commun 2016; 7:13119. [PMID: 27721490 PMCID: PMC5062559 DOI: 10.1038/ncomms13119] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 09/05/2016] [Indexed: 12/28/2022] Open
Abstract
For a cell to move forward it must convert chemical energy into mechanical propulsion. Force produced by actin polymerization can generate traction across the plasma membrane by transmission through integrins to their ligands. However, the role this force plays in integrin activation is unknown. Here we show that integrin activity and cytoskeletal dynamics are reciprocally linked, where actin-dependent force itself appears to regulate integrin activity. We generated fluorescent tension-sensing constructs of integrin αLβ2 (LFA-1) to visualize intramolecular tension during cell migration. Using quantitative imaging of migrating T cells, we correlate tension in the αL or β2 subunit with cell and actin dynamics. We find that actin engagement produces tension within the β2 subunit to induce and stabilize an active integrin conformational state and that this requires intact talin and kindlin motifs. This supports a general mechanism where localized actin polymerization can coordinate activation of the complex machinery required for cell migration. The role of force in activating integrin cell adhesion receptors is not known. Here the authors develop fluorescent tension sensors for αL and β2 integrins and show that in migrating T cells force is transduced across the β2 integrin, and that this correlates with an active conformational state.
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Affiliation(s)
- Pontus Nordenfelt
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Program in Cellular and Molecular Medicine, Children's Hospital Boston, 3 Blackfan Circle, Boston, Massachusetts 02115, USA.,Image and Data Analysis Core, Harvard Medical School, 240 Longwood Ave., Boston, Massachusetts 02115, USA.,Department of Clinical Sciences, Division of Infection Medicine, Faculty of Medicine, Lund University, BMC, B14, Sölvegatan 19, 22362 Lund, Sweden
| | - Hunter L Elliott
- Image and Data Analysis Core, Harvard Medical School, 240 Longwood Ave., Boston, Massachusetts 02115, USA
| | - Timothy A Springer
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Program in Cellular and Molecular Medicine, Children's Hospital Boston, 3 Blackfan Circle, Boston, Massachusetts 02115, USA
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